The Trump administration’s chief strategist has already taken control of both policy and process on national security.

Steve Bannon, chief strategist and senior counselor to US President Donald Trump, attends a meeting with automobile leaders in the Roosevelt Room of the White House in Washington, DC, January 24, 2017. / AFP / SAUL LOEB (Photo credit should read SAUL LOEB/AFP/Getty Images)

If there was any question about who is largely in charge of national security behind the scenes at the White House, the answer is becoming increasingly clear: Steve Bannon, the former head of Breitbart News, a far-right media outlet, and now White House advisor.

Even before he was given a formal seat on the National Security Council’s “principals committee” this weekend by President Donald Trump, Bannon was calling the shots and doing so with little to no input from the National Security Council staff, according to an intelligence official who asked not to be named out of fear of retribution.

“He is running a cabal, almost like a shadow NSC,” the official said. He described a work environment where there is little appetite for dissenting opinions, shockingly no paper trail of what’s being discussed and agreed upon at meetings, and no guidance or encouragement so far from above about how the National Security Council staff should be organized.

The intelligence official, who said he was willing to give the Trump administration the benefit of the doubt when it took office, is now deeply troubled by how things are being run.

“They ran all of these executive orders outside of the normal construct,” he said, referring to last week’s flurry of draft executive orders on everything from immigration to the return of CIA “black sites.”

After the controversial draft orders were written, the Trump team was very selective in how they routed them through the internal White House review process, the official said.

Under previous administrations, if someone thought another person or directorate had a stake in the issue at hand or expertise in a subject area, he or she was free to share the papers as long as the recipient had proper clearance.

With that standard in mind, when some officials saw Trump’s draft executive orders, they felt they had broad impact and shared them more widely for staffing and comments.

That did not sit well with Bannon or his staff, according to the official. More stringent guidelines for handling and routing were then instituted, and the National Security Council staff was largely cut out of the process.

By the end of the week, they weren’t the only ones left in the dark. Retired Marine Gen. John Kelly, the secretary of homeland security, was being briefed on the executive order, which called for immediately shutting the borders to nationals from seven largely Muslim countries and all refugees, while Trump was in the midst of signing the measure, the New York Timesreported.

The lack of a paper trail documenting the decision-making process is also troubling, the intelligence official said. For example, under previous administrations, after a principals or deputies meeting of the National Security Council, the discussion, the final agreement, and the recommendations would be written up in what’s called a “summary of conclusions” — or SOC in government-speak.

“Under [President George W. Bush], the National Security Council was quite strict about recording SOCs,” said Matthew Waxman, a law professor at Columbia University who served on Bush’s National Security Council. “There was often a high level of generality, and there may have been some exceptions, but they were carefully crafted.”

These summaries also provided a record to refer back to, especially important if a debate over an issue came up again, including among agencies that needed to implement the conclusions reached.

If someone thought the discussion was mischaracterized, he or she would call for a correction to be issued to set the record straight, said Loren DeJonge Schulman, who previously served in former President Barack Obama’s administration as a senior advisor to National Security Advisor Susan Rice. Schulman is now a senior fellow at the Center for a New American Security.

“People took the document seriously,” she said.

During the first week of the Trump administration, there were no SOCs, the intelligence official said. In fact, according to him, there is surprisingly very little paper being generated, and whatever paper there is, the NSC staff is not privy to it. He sees this as a deterioration of transparency and accountability.

“It would worry me if written records of these meeting were eliminated, because they contribute to good governance,” Waxman said.

It is equally important that NSC staff be the ones drafting the issue papers going into meetings, too, said Schulman. “The idea is to share with everyone a fair and balanced take on the issue, with the range of viewpoints captured in that document,” she said.

If those papers are now being generated by political staff, she added, it corrupts the whole process.

It could also contribute to Bannon’s centralization of power.

“He who has the pen has the authority to shape outcomes,” the intelligence official said.

Now Bannon’s role in the shadows is being formalized thanks to an executive order signed Saturday by Trump that formally gives Bannon a seat on the National Security Council’s principals committee. The same executive order removed from that group the chairman of the Joint Chiefs of Staff, the director of national intelligence, and the secretary of energy. Their new diminished role is not unprecedented, but some still find it a troubling piece of this larger picture.

For example, former Defense Secretary Robert Gates — who served under both Bush and Obama — told ABC News this weekend that sidelining the chairman of the Joint Chiefs and the director of national intelligence was a “big mistake.” Every president can benefit from their “perspective, judgment, and experience,” Gates said.

Meanwhile, Bannon’s new role is unprecedented. Under Obama, it wasn’t unheard of for his chief political advisors, John Podesta and David Axelrod, to attend NSC meetings, but they were never guaranteed a seat at the table. Under Bush, the line between national security and domestic political considerations was even clearer. Top aides have said they never saw Karl Rove or “anyone from his shop” in NSC meetings, and that’s because Bush told him explicitly not to attend.

The signal Bush “especially wanted to send to the military is that, ‘The decisions I’m making that involve life and death for the people in uniform will not be tainted by any political decisions,’” former White House Chief of Staff Josh Bolten said last September.

Sen. John McCain (R-Ariz.) called Bannon’s appointment to the council as a permanent member a “radical departure” from how the decision-making body was organized in the past, adding that he found the change “concerning.”

Inside and outside of government, there are also deep reservations about Bannon’s alignment with the far right and white nationalism, thanks to his previous leadership of Breitbart. One Bannon quote making the rounds this weekend: “Lenin wanted to destroy the state, and that’s my goal, too. I want to bring everything crashing down and destroy all of today’s establishment.”

There are new questions about where retired Army Lt. Gen. Michael Flynn, Trump’s national security advisor, fits into all of this. Internally, it remains unclear what his role is, the intelligence official said. “He has a voice at the table, but he’s overshadowed by Bannon.”

Meanwhile, Tom Bossert, a former Bush national security aide whom Trump picked to serve as the White House’s homeland security advisor, is not “one of Bannon’s,” so he is also on the outside looking in, according to the official. However, in Saturday’s executive order, Bossert was also given a permanent seat on the NSC principals committee.

But there is not a lot of infighting right now, because to have infighting, there needs to be a power struggle, and there is no struggle, the intelligence official said.

However, there is an effort to crack down on leaking. Last week, a draft executive order, which raised the prospect of bringing back CIA “black sites” and reopening the debate on torture, leaked to the press. White House Press Secretary Sean Spicer said it was “not a White House document” and that he had “no idea where it came from.” But according to the New York Times, “the White House had circulated it among National Security Council staff members for review on Tuesday morning.” The Times was even provided with the details of the email chain that showed “the draft order’s movements through the White House bureaucracy.”

“They’re doing a witch hunt now to find out how that got out,” the intelligence official said. “There is zero room for dissenting opinion.”

Trump did say publicly that he would defer to Defense Secretary James Mattis for now on the question of torture, which would suggest that disagreement is OK. But while publicly the president is allowing for different opinions, there is unhappiness about what is permitted behind the scenes, according to the official. If you take a stand against the White House, you might find yourself frozen out of future meetings, he said.

The NSC staff is mostly in shock after last week, the intelligence official said. For now, no one knows what each day will bring. There is no organizational chart yet for the NSC, meaning there has been no internal guidance yet about which portfolios still exist and to whom they report, the official said. The Washington Postreported Sunday on some of the changes being made, including that “some offices such as cyber have been expanded, while others have been collapsed.” The directorates on Europe and Russia, which were separate under Obama, have now been combined.

It’s possible that the current chaos and lack of bureaucratic process is a result of the Trump administration still going through growing pains and figuring out how best to run things. But former NSC officials said an organizational chart for the NSC is the kind of thing you have in place weeks before taking office.

Only time will tell if the way things are currently being done is deliberate or part of a new administration learning on the job how best to provide advice to the president and communicate with the relevant agencies.

Trump’s management style is known to be highly unstructured, if not chaotic. The Postreported in May that he was running his presidential campaign like he ran his business — “fond of promoting rivalries among subordinates, wary of delegating major decisions, scornful of convention and fiercely insistent on a culture of loyalty around him.”

“While this may have worked for his company, it is certainly not a way to run a country,” the official said.